The X-Files: Beyond The Truth (10x01)
by espresso651
Summary: With Mulder and Scully in hiding, the loss of two Deputy Directors, and the War on Terror, the new FBI Director along with AD Skinner investigate corruption within the FBI while Doggett, Reyes, and Reyes' new partner follow clues that might lead them to Mulder and Scully.
1. Introduction

The X-Files 10x01 – Beyond The Truth

Disclaimer: The names, addresses, locations, emails, URLs, web sites, and software mentioned in this are fictional. Any resemblance to actual people, places, or other details is coincidental.

Introduction

I wrote this several years ago as a writing exercise between short stories. My intent was to make a satisfying, imaginary 10th season premiere episode to The X-Files that picked up some time after the final episode, The Truth. So I called the episode Beyond The Truth, since it would introduce a story arc to resolve that episode.

I wanted to tell a story that felt like the 3rd season, but the ending of the series left me with a problem. Mulder and Scully were in hiding in Europe, there was turmoil in the FBI, and there were characters who were left hanging there like chads on an election ballot. The story needed resolution, and for that, Mulder and Scully needed to be shadows. So I ended up making a story that was meant to feel like classic X-Files, but without Mulder and Scully's immediate presence.

This story is cleanup from the mess that was the ninth season, and in effect, an attempt at redeeming the misuse and bad writing of certain characters. I hoped that even characters I hated, such as Kersh, would come off as more interesting in writing this, even when characters don't appear.

So I never wrote this to be read, but I have shared it a few times and it has gotten a positive reaction. Hopefully you'll enjoy this episode that was never aired.


	2. Teaser

Teaser

April 2, 2003, 4:36 PM, New Orleans, Louisiana.

Some kids are playing on a playground. An unmarked van is parked across the street watching. One of the parents notices the van, and whispers to her friend. They look uneasy. "You should call the cops." one of them says. The woman gets out her cell phone and dials 911.

A police car shows up, and asks what is going on. She points to the van, where someone appeared to be watching the children from the passenger seat. The face then turned and said something to someone else in the back. The cop tells his partner to wait, he would check it out.

The cop goes to the driver's side door, and taps on it. The passenger does not roll down the window, he just snarls, pulls out a gun, and shoots the cop in the face.

The partner calls in "shots fired" and pulls out his gun. He goes toward the van, while the driver gets out of the back and rushes to the driver's seat. The cop shoots out the front passenger side tire, and the passenger points the gun out of the window and fires at the cop. He misses. The cop shoots at the passenger, hitting him in the shoulder, causing him to drop the gun and fall over into the driver's lap. The cop moves for cover, while the driver struggles to get his fallen associate off of him. Then the driver throws open his door, and falls out. He picks himself up and starts running, the cop chasing after him. He runs down an alley, and jumps the fence. The cop tries to catch up, but he's gone.

He goes back to the van, and two more cars have arrived. The area is secured, and the police are taking witness statements. The passenger is in custody. The cop and another officer open the side door to the van, weapons drawn. Inside, they find nothing to shoot. Instead, there is an entire wall of electronic equipment, and several monitors. One showed a video feed of a teenager in his room, on a computer. A pair of headphones played the audio from the room. Another monitor showed a web browser apparently moving by itself, navigating a website on the 2012 apocalypse. "What the hell is all this?" the second officer said.


	3. Act I

Act I

April 4, 2003, 11:21 AM, New York City

A man is sitting at a desk watching people enter a building. He is wearing a uniform and armed with a gun. His hair is cut short, like a crew cut, and he has a hardened expression on his face. He is surrounded by monitors, which show different parts of the building. On his right chest is a nametag labeled "Doggett."

He notices an unusual figure enter the building. He is wearing a long trenchcoat, and Doggett senses a certain rhythm to his movements. He looks like a dangerous figure, either law enforcement or criminal underworld. He is approaching Doggett.

The man comes near Doggett's station. "John Doggett?"

"Yeah. Who's asking?"

"Agent Tolson, FBI." He pulls out a badge.

"FBI…"

"The director needs to speak with you. It's urgent."

"I've got nothing to say to him. You tell him that."

"Sir, he said it was very important. I was to bring you in, under any circumstance."

"What the hell is this? I'm on duty now."

"We've made arrangements for that."

Doggett could see Raines, his night relief, entering the door. "So I don't have a choice in this?"

"No, Agent Doggett. You do not. Please come this way, before we draw a crowd."

"Right…" Doggett muttered as he started to follow the agent out.

3:22 PM, FBI Headquarters, Washington, DC

Doggett and Tolson headed down the corridor toward the director's office.

"Tolson, huh? Family connection?"

"No sir, just a coincidence."

"I see. Some coincidence."

"We're here."

"I know, I used to work here."

"Yes, sir. The director is waiting."

Doggett entered the door where a receptionist sat at a desk. Tolson spoke. "John Doggett here to see the director."

"I will let him know." She got on her phone and told the director that John Doggett was waiting. "Come this way, Mr. Doggett." She led Doggett into the office, while Tolson left. Inside there were three people seated around the director's desk. The director himself, an older, once-blonde woman, and an irritated-looking man with a shaved head and glasses.

"Agent Doggett, have a seat." Said the man behind the desk.

"I'm not an agent anymore. I quit, remember."

"Have a seat. We need to talk about an incident that happened."

"And what 'incident' would that be?"

The bald man spoke up. "This is important, John."

The director answered him. "The murder of a military intelligence officer, Knowle Rohrer."

"Knowle Rohrer? That's already been covered, covered-up, and stamped with a nice seal of approval from this office. You looking to pin it on more people now?"

"Relax, Agent…Mr. Doggett. It seems some concerning things happened in my predecessor's time in this office. We just want the truth."

"You got the truth. Fox Mulder spelled it out for you, and this office shut him up. Wanted him dead."

"Yes. Yes, this office wanted him dead. That was then. Things have changed now."

"I'll bet…"

"AD Skinner has been alerting me to some concerning things. Allegations of corruption reaching far outside this office, military tribunals being held off-the-record on civilians, unauthorized records maintained on American citizens. Agent Doggett, this is a time of war. We're dealing with an outside threat looking to undermine the nature of America itself. Now I find out this office is part of that threat?"

"Surprised?"

"I've looked at some of the files outside of your "X-Files" project. We've had agents disappear. One agent affiliated with this alleged corruption, Alex Krycek, had close ties to Russian organized crime before he disappeared. An assistant director implicated in corruption was arrested for homicide. Another assistant director committed suicide before the conclusion of an investigation that you started."

"Excuse me? I closed my investigation into AD Kersh."

"You did. It was reopened after the Rohrer incident."

"On whose authority?"

The director turned to AD Skinner. "My authority, John."

"Even after…"

"That's not your concern."

The director spoke again. "It's clear crimes were committed within these walls. The nature of these crimes remains unclear. What is clear is that the danger they represent is a threat to the safety and security of the United States. That makes it my interest."

"So what do you want from me then?"

"The truth, Agent Doggett."

After the meeting, Doggett was walking away from the office. A voice from behind him shouted to him. "John, stop."

"So it's John now, Skinner?"

"I wanted to thank you."

"Thank me? Dragging me out here to say what they already know?"

"To thank you for speaking the truth. It's getting harder to do that here."

"Why is that?"

"The people in charge don't want the truth. They want…something else."

"This new director, you trust him?"

"Do you have to ask that?"

Doggett nodded.

"This is about Agent Mulder."

"Mulder? He's gone. You know it. I know it. Leave him out of this."

"They don't want him now. They're occupied with Bin Laden and al-Qaida. He's not even on their radar."

"Good for him. I hope he enjoys having them off his tail."

"It's not the bureau he has to worry about. Whether he knows it or not, he's stirred up a shitstorm here. He's a wanted man outside of the FBI."

"What's this got to do with me?" Doggett asked.

"I need you to warn him. I have a message for him."

"You expect me to track him down?"

"I expect you to save his life."

"Resigned, remember. I threw my badge on Kersh's desk and told him where to shove it, Skinner."

"That's why I still trust you."

9:31 PM, New York City – Doggett's Apartment

Doggett entered his apartment and removed his jacket. His apartment was small and modest, and well kept. Not a lot of pictures or decorations, other than a picture of his son near the phone. He immediately went to the fridge and grabbed a bottle of beer. While he wrestled the cap off, he went to the answering machine, which had a message on it. He played it, and a female voice spoke. "John, I need to talk to you. Call me at the office. Or call my cell. This is important." It was a voice he had not heard in months, from a life he was trying to escape from.

He took a swig from the bottle, then picked up the phone.


	4. Act II

Act II

April 4, 2003, 9:39 PM, New York City – Doggett's Apartment

"John?"

"Monica. What's going on?"

"It's good to hear from you. Are you doing okay?"

"Yeah, yeah, what's this about?"

"It's about…our friend."

"Mu…"

"Our friend."

"Yeah. You're not the first to mention that to me today."

"They talked to you already?"

"Yeah they did."

"They spoke with me this morning. We need to talk."

"Down there?"

"I'll meet you up there. Tomorrow afternoon."

"Where?"

"It's your city, John."

"Okay. There's a deli on 5th. Dean's."

"Done."

"Monica,"

"Yes?"

"Be careful. Skinner was trying to warn me about something. Watch where you stick your head."

"I will. Take care."

"Good night, Monica."

April 5, 2003, 2:03 PM, New York City

Doggett was sitting at the table with a turkey sandwich. No sign of Agent Reyes yet. It was an abnormally slow day at the deli. There was only one customer in line. That customer was a young woman with long black hair. After she got her sandwich, she walked over to Doggett's table and sat down. "Hi there. You look like you could use some company."

Doggett looked at her coldly. "I'm waiting for someone."

"I can see that. I can keep you company until she, I guess it's a she, get here."

"I can eat by myself."

"Or we could talk. Lots to talk about these days. Guns, glory, magnetite."

"What did you say?"

"Magnetite. Nice stuff. Makes your problems stay away, am I right?"

"Who are you?" He was tensing up, and wishing he had his gun.

"A friend. Well, a friend of a friend. A woman you knew once. Worked very closely with. She sent me to find you."

"Who…"

"Shh. I'm just supposed to give you this, Agent Doggett." She pulled out a folded piece of paper. "Trust no one, John." She kissed him on the cheek, and then picked up her sandwich and walked out the door.

A voice spoke to him. "I see New York is treating you well, John."

"Monica? Where have you been?"

"New York traffic. And my flight was delayed. Who was that?"

"She said she's a friend. A friend of Scully. She gave me this." He showed her the paper.

"What's it say?"

"I haven't read it."

"Well…"

He opened the paper. It only showed an address and a time. It was a location in Milton, Vermont. The time was Sunday, 0900.

Monica spoke. "So Scully's in Vermont?"

"It would seem. I thought they were overseas."

"That's what I'm here to tell you about."

"What have you got, Monica?"

"We got a report from the NOPD, the local police, about a cop killing."

"God…"

"Well it wouldn't have been our concern except that they found something at the scene. The killer was wiretapping and spying on someone."

"Who?"

"Some kid. Nobody. They handed it over to us. It was extensive, what they did. Video cameras all over his house, they were stealing the family's mail, the phone was tapped, keyloggers and backdoor software was installed on the computers. The kid's computer had it the worst, every action was being recorded remotely. Every website, every password and login, they had everything on this kid."

"What did they have?"

"This." She pulled out a folder. Doggett looked through it. It was chat logs and emails to and from trustnoone . "Mulder?"

"That's what I think. I'm pretty sure that what they thought, too."

"Why is Mulder chatting with some kid?"

"He runs The Dark Archive. A website for declassified government information."

"Mulder's kind of thing."

"Exactly."

"So what does this have to do with me?"

"The bureau has this information now. They can trace Mulder. They have this kid's credentials. They can pretend to be him."

"You mean they can smoke Mulder out?"

"Precisely."

"Monica, Skinner, and the director, told me they weren't interested anymore."

"They lied, John."

"Skinner?"

"Who do you trust now, John? Mulder and Scully are gone."

"I trust you. I always trust you."

"Thank you. Sometimes I don't trust myself anymore."

"We can't give up like that. We can't be like…like Mulder."

"Well I want you to have these."

"What? This is bureau property."

"I know. And I can't let them have it."

"This is serious, Monica."

"And it's Mulder's life we're talking."

"Fine. And what do I do with this? I'm a civilian."

"Find him. Finish what he started."

"And you?"

"I'm going to bury this. Keep them off the trail until you find them. Then I'm going with you to Vermont."

"Alright. You just be careful."

"That's what I was going to tell you."

"You know they aren't done. The Super Soldiers, I mean."

"I know. That's why I need you on this."

In a car parked down the street, a man in a trenchcoat listened in. He picked up his phone and dialed a number. "We've got a trail. JD will lead us right to them. I need everything I can get on this Agent Monica Reyes. She may be a problem." The voice was that of Agent Tolson.

FBI Headquarters, 3:43 PM

"Skinner, thanks for coming."

The assistant director sat in the chair across from the director. "What can I do for you?"

"I'm concerned about what Doggett told me. Is he honest?"

"His integrity is beyond question, as far as I'm concerned."

"But aliens? That look human? Come on, Skinner. This is insane."

"His report is consistent."

"Yes. I know. I've read. It's all consistent. What I want to know, is who they are."

"I believe Mulder's statements…"

"I'm not interested in Mulder's statement. He's nuts. The man's a lunatic. He infects everyone around him with lunacy. I'm not interested in chasing Dracula with wooden stakes when dirty bombs are going off in airports."

"Sir, I…"

"Skinner, I need to know who I can trust."

Skinner was silent.

"Well? Who can I trust?"

"A friend once told me, trust no one. I think he was right."

"Times like these, I can believe that. I want to know, Skinner, can I trust you?"

"Mr. Director, I don't believe I can trust you."

"That, I do believe. I appreciate that. I have something I need you do to."

"What is that?"

"I want the 'truth' here. No more of this alien crap. I want to know who is running the show, who is pulling the strings, and if there is any reason to suspect terrorism. I need you to head an investigative unit on these matters."

"Am I to understand you are re-opening The X-Files?"

"No, never. You will operate in secret, and this is in addition to your other duties. Officially, this is a counter-terrorism unit. I will leave it to you to run this one, but I want to know how far this corruption goes. Who is funding it, what it's tied to."

"Fine. I want Monica Reyes on the team."

"Your call. She was part of the X-Files project at one time, correct?"

"Yes sir."

"I see. Remember, Skinner, this is not the X-Files."

"Sir, her record is exemplary, her work on unusual crimes…"

"Yes. That is noted. I want this group organized by Monday. You have the weekend to get this moving."

"Is there anything else?"

"Yes, there is. I want someone on your team."

"Who is that?"

"Agent Michael Tolson. Former NYPD, he helped take down the Torino crime family a few years back. He's been with us a few years now, a rising star. Heard of him?"

"Heard of him. Never met him."

"He's met with me a few times. A lot of connections, that boy has. He does good work."

"Connections aren't what's important…"

"No, but it legitimizes the work. He's good. He'll be a powerful asset."

"Yes sir."

"That is all. Dismissed."

JFK International Airport, 7:10 PM

Monica Reyes was walking toward the terminal, not aware of the man reading his newspaper as she walked by. He lowered the paper enough to watch her, then whispered into his pocket. Another man across the hall nodded, and began walking in her direction. Reyes showed her ticket at the gate, and the woman there told her to step aside. A TSA agent was waiting there.

She went to the TSA agent, who looked her over suspiciously. "Are you carrying any weapons?"

"I am an FBI agent, and I have my gun."

She reached for her badge, and the man looked horrified. "Don't you move."

"I am a federal agent, and I am reaching for my badge."

He called on his radio for help. Reyes thought to herself this was very strange. Things were tense in the last few weeks because of Iraq, but she had never seen a reaction like this. Meanwhile, the man who was following her approached, with the man reading the newspaper close behind. "I've got this. Ma'am, you'll need to come with us."

"Who are you? I'm a federal agent on official business…"

He pulled out a gun. "It will be easier on everyone if you just come with.."

She kicked him in the chest and ran. "Get her!" he shouted to his newspaper-carrying friend.


	5. Act III

Act III

She was running through the airport, with the gun-wielding man and a TSA agent following. She ran into a women's bathroom. They were still in pursuit. She grabbed her phone, and called the first number she could think of. While it rang, she pulled out her gun. As soon as there was an answer, she shouted "This is Agent Monica Reyes, I need assistance at JFK International Airport. They are armed and dangerous." The man came through the door, recovered from the kick. She ran into a stall. He moved in, and cornered her. "You little…"

"Don't even finish that sentence!" she ordered, pushing her gun into his face. "Drop your weapon, I am a federal agent."

"Do we go in? Do you have her?"

She pushed the barrel of the gun into his forehead. "Tell them to stand down."

"Wait outside. Cover the door." He told them.

"Now, who are you? Who sent you?"

He was silent. So she shouted, "Who the hell are you?"

"NSA."

"Bullshit."

"Ms. Reyes, we were ordered to bring you in. It's a matter of national security."

"I'll bet. Who are you really?"

"This won't…"

"Start talking, or I'll finish this."

Another voice came in. "Agent Reyes, do you need assistance?"

"Who's there?"

"Special Agent Curtis, we're here to assist."

"The men outside?"

"We've got them. What's your situation?"

"One man inside, he's armed."

"Roger. We're coming in."

Three agents stormed in, guns drawn. Two of them pointed their guns at the assailant, and one of them went to Reyes. "Agent Reyes, are you okay?"

"Yes, I'm okay. Any idea what's going on?"

"I was hoping you could tell me. The other men were heavily armed, we don't know how they got through security. No ID on them. They won't identify themselves."

"He said he was NSA."

"We'll look into that. So what happened?"

"I was checking in, and they sent to the a security checkpoint. I identified myself, and the agent freaked out, and these men appeared with guns."

"We've got the man who stopped you at security. He's in a TSA uniform, but the security here says they've never seen him before. Like the others, he had no ID."

"What is going on here?"

"I don't know, but someone important wants to talk to you."

9:39 PM, FBI Field Office, New York City

"Agent Reyes, how are you holding up?"

"I'm fine. Thanks."

"Thank God. I needed to get in touch with you, but this isn't what I had in mind."

"It wasn't my plan for the evening, either."

Skinner seemed stressed and relieved at the same time. "What happened there?"

"Someone stopped me from getting on my flight. They said they were NSA. No ID on them. The NSA denies involvement."

"I'll check into that. You get some rest. I'll inform the New Orleans Office of your whereabouts."

"Actually, I'd prefer you didn't."

"Why is that?"

"It's…private."

"I see. I don't like this subterfuge. I will meet you up there in the morning. We need to talk."

"Alright."

"I'll have agents escort you. Someone wants you dead, and I won't let that happen."

"Thanks. Thanks for your help."

"Just be safe, Agent Reyes. I've lost too many good agents lately."

April 6, 8:14 AM, New York City

Skinner entered Reyes' room while she was sitting, drinking coffee and looking down at the city below. "I never gave this city much thought. It's so busy and feels so angry. It looks different from here, like it's truly alive."

"Agent Reyes, about last night…"

"Yes. Did you find anything?"

"The man in the uniform is Alvin Morin, he's got a long history. He was a hitman for a crime family here before we took them down. We didn't pursue charges on him because he was already in jail for burglary. He was an informant."

"The mafia?"

"Something like that. I want you to meet someone. Agent Tolson, come in."

The agent entered. "Agent Reyes, I heard about what happened. I am so sorry. I hope you are okay."

"I'm fine, thanks." Something unnerved her. She couldn't place it.

Skinner spoke. "Agent Tolson will be your new partner. I am reassigning you."

"Reassigning? To what?"

"A new project. Classified. Counter-terrorism."

"I don't handle terrorism cases."

"You do now. This is your assignment."

"And the cases I'm working on?"

"Already reassigned."

She looked frustrated. "There's a case I can't leave right now."

"Why is that?"

"Because…it relates back to…"

"The X-Files?"

"Essentially."

"Agent Reyes, The X-Files are closed. End of discussion."

"I see." She said, resigningly.

Tolson spoke up. "Agent Reyes, I have some history with this Morin. When I was NYPD, I helped bust him. He knows me. I want to check out his old haunts, find out who he's been dealing with. Are you up to it?"

"As an assignment?"

Skinner answered. "As your first duty in your new assignment. Someone wants to kill FBI agents. We need to know why. You will not be going alone, because I realize you are the target here. I will be sending agents Curtis and Alley to shadow you."

"Skinner, may I speak with you in private?"

Skinner signaled for the other agents to leave.

"I met with John last night. This is just between us. Someone gave him some information."

"What kind of information?"

"We don't know yet."

"You don't know?"

"We need to go somewhere. Tomorrow morning. This investigation you've got me on, it will have to wait."

"It can't wait."

"It has to. John told me you knew something important. That would save the life of Mulder. This is our only shot."

Skinner thought for a second. "Alright. I'll handle this. You meet with Doggett. Just remember, he's out of the bureau now. He doesn't work for us."

"That's why I trust him."

"I want you to look this over when you can." He handed her a file. It was Tolson's personnel file.

"Light reading?"

"I want you to know who you are working with. He's a good agent. He plays by the book."

"Charming."

"I'll tell him you're off the case for the next few days. I want to hear back from you Tuesday morning."

"Got it."

Without saying anything else, Skinner left. The agent assigned to guard her came back in. "You've got some powerful friends at the bureau." The agent remarked.

"It comes at a price."

"I'd pay it."

10:13 AM, New York City

John Doggett was at his desk watching the monitors, when Reyes entered the building. "Hi John." She said.

"Monica. I thought you went home."

"So did I. Long story. We've got a lot to talk about."

"Yeah, well I've got a lot to tell my boss, too. He's not thrilled with the feds running around pulling his staff and forcing overtime."

"You can't be enjoying this. Don't you miss it?"

"Beats chasing black oil across the world and getting hit in the head every few days."

"You have a point."

"So what brings you here?"

"I met with Skinner this morning. I've also been reassigned."

"Reassigned? What to?"

"Classified. War on Terror stuff. Or something."

"Spooky."

"It is, John. I don't even know my assignment, and I don't like it."

Doggett looked at her with concern. "You could quit."

She thought for a second. "I can't do that. Someone has to keep searching."

"The X-Files are gone, Monica. They aren't coming back."

"Yes, but the truth is still out there."

"Yeah, okay. The truth. I'll believe that. I just don't want to see you in an orange jumpsuit at a mock trial in some army base."

Reyes changed the subject. "So, Milton. When do we leave?"


	6. Act IV

Act IV

April 6, 11:26 AM, New York City

Skinner was inside a restaurant talking on his phone. In the car, Agent Tolson was watching from the side window. He was also on his phone, talking to another person. "She's not here. We have to wait."

On the other end, another voice was irritated. Tolson didn't seem affected by it. "We'll deal with it. We've got another problem. I won't be coming alone. Bald guy. Don't ask."

The other voice kept talking, but Skinner was leaving the restaurant. "I have to go. Be ready." Tolson told the voice on the other end.

Skinner entered the passenger side. "Dead end. He didn't know anything."

"This guy, he's close to a lowlife I busted, Buddy Turner. Runs a body shop in Queens. We should check it out."

"Okay. What do you know about him?"

"Oh, everything. Guy's a nutcase. Nothing we could prove in court, though. Tried to shoot a man at his shop, got off on self-defense."

"Well let's not get ourselves shot here."

"I think he knows better than to shoot a fed. And we've got them, too." He nodded toward the unmarked car that was tailing them. Then he pulled out onto the street and they drove off.

12:59 PM, Queens

They didn't see the sign for the rundown auto shop first, they saw the flashing lights. Two police cars were outside of the shop. "Guess we're not the only ones wanting a word with old Buddy." remarked Tolson.

"Let's see what's going on." Said Skinner, cautiously. They stopped the car, and had their badges out before getting out of the vehicle. "FBI." Skinner said to the cop outside.

"Didn't call the feds on this. What's going on?"

"We needed to ask Mr. Turner some questions."

"You can ask all you want, that corpse won't be opening his trap."

Tolson spoke. "He's dead? How?"

"Suicide. Blew his head off. Couldn't happen to a nicer guy, you know?"

Skinner then cut in. "We need to see the scene."

"Knock yourselves out. Right in there."

Down the street, the unmarked car was watching. A scruffy looking man in dirty clothes banged on the driver's side window. "Hey man, roll it down." He kept knocking on the window. "Some change?" The agent rolled his eyes, and his partner, Agent Alley, gave a quick laugh.

"Curtis, you're a cheap-ass." He reached into his pocket and grabbed a few quarters.

"Agent Alley, we have an assignment. And you're only encouraging him."

"Sure. Roll it down." He began to move the change-filled hand over his partner.

"Fine." Curtis rolled down the window, and the man clasped his hand over Alley's.

"Bless you." He smiled as he said it. Only instead of taking the money from his hand, he squeezed it and pulled, and his other hand revealed a gun pointed right at Agent Curtis' head.

Inside the auto shop, two cops were standing around, seemingly doing nothing. Skinner had identified himself, and he and Tolson were looking around. "Hey boss, check this out." Tolson found a sheet of paper. It said "Morin – Hill 5 PM Shaggy's". "Looks like our guy was gonna get a crappy burger with our other guy. And Hill was in on it."

"Okay, who is Hill?" Skinner asked.

"Oh he's…my God…" Tolson did not finished the sentence before his gun was drawn, and Skinner turned to see the cops aiming their weapons directly on him. "Good night, G-man." One of the cops said as he fired. The bullet went into Skinner's shoulder, and the next sound he heard was "you son of a bitch!" from the mouth of Agent Tolson, who fired into the cop's chest. Outside, he heard two shots fired. "You killed Danny!" the other so-called cop screamed, and fired clumsily at Tolson, missing the target. Tolson charged at the cop, knocking him down. Skinner held his wounded shoulder and found himself unable to get up. A figure came through the door, while Tolson and the cop wrestled for control of the gun. It was the cop from outside. "You dirty prick, now you're going to…" One more shot was fired.

2:30 PM, New York City, Doggett's Apartment

Doggett and Reyes were staring at a computer screen, and Doggett was at the keyboard. They were looking at an email program sending a message to the address trustnoone .

Subject: Your safety

Dear Spooky, this is a friend. I need to warn you that The Dark Archive has been compromised and your identity has been discovered. Do not trust any messages from The Dark Archive or its founder.

I also have a message from someone close, it is very important. You are not safe where you are. I will meet your partner at the rendezvous as planned.

"Do you think it's enough?" Doggett asked.

"It has to be. I just hope he reads it before something happens."

"We'll tomorrow we'll find out what Scully wants."

"Yeah."

Reyes' phone rang. "Agent Reyes."

"Reyes, this is Tolson. I have some bad news. About the assistant director."

"Skinner? What happened?"

"We were ambushed. Skinner was shot."

"Shot? Was he..." Doggett's eyes opened at the sound. Someone shot Skinner? He almost interrupted, but she stopped him with a hand gesture.

"He's in the hospital. It would have been worse. Curtis is dead. Alley is critical. It was Alley, he shot the guy who was going to kill Skinner."

"So, so do they think Skinner is going to be okay?"

"We don't know. Where are you?"

"I'm…investigating. Something." She realized how bad that sounded.

"What is it? We're working this together, remember?"

"Yeah, look, this is something private. It's between me and the assistant director."

"Who is laying in a hospital getting ready for surgery, and can't speak for himself now. You have to trust me." That last sentence rang in her ears. Something felt wrong.

4:12 PM, Wilkes Memorial Hospital

Doggett and Reyes walked down the corridor, and saw two agents standing by a door. Tolson was sitting nearby, and got up when he saw them approach. "Mr. Doggett, good to see you again. Agent Reyes."

Reyes spoke first. "Any word?"

"It's not life threatening. He will be out for a while."

Then Doggett asked "So what really happened there?"

"Mr. Doggett, that's part of an official investigation, and you're not an investigator."

"No, but I am. I want to know how it went down." Reyes said.

"Well we were checking a lead on the Morin matter…"

"Alvin Morin?" Doggett asked.

"Yes. We were checking it out, and were ambushed by some hit men."

"Who were they?" Reyes asked.

"We don't know. Just like before, only these guys weren't in the system. We're waiting on more results, but I'm not expecting much."

Doggett then said, "So you're tying all this to Morin? To the Torino mob?"

"Mr. Doggett, this is an FBI investigation."

"And I worked those cases for the NYPD."

"So did he, John. Agent Tolson was with the New York police too."

"Mr. Doggett, this isn't a pissing match. It's protocol. You're not FBI."

"But he's involved in the case, Tolson. He's with me, as a consultant." Reyes argued.

"Fine. Now, we need to find out who did this one, too. This is turning into a huge conspiracy."

"Don't they always…" Doggett remarked.

"We can't. We have to go." Reyes said.

"Where? This is the priority."

"Agent Tolson, people have died. More people will die. Unless we can do this one thing."

"I can't help you, Agent Reyes, if I don't understand. We're a team now. And I guess he's along for the ride, too. Just tell me where we are going, and we'll get there."

Doggett and Reyes looked at each other.

April 7, 9:10 AM, Milton, Vermont

It was a quiet Sunday morning at the park. Doggett sat on a bench, waiting. He checked his watch, it was past nine already. Where was Scully? Down the street, a car was parked with two people inside. Agent Reyes in the driver's seat, and Tolson in the back. Reyes was using her cell phone to check an email address she had set up the day before. There was a message, from trustnoone . Two simple words. "What rendezvous?"

Doggett was getting worried. He muttered to himself "damn it Scully. Where are you…" where no one could hear. He was startled when a voice spoke from behind him.

"Hello, John." He turned, and did not see the woman he expected to see. Behind him was Shannon McMahon.

"Shannon?"

"We've got a lot to talk about."

 _To be continued…_


	7. Afterword

Afterword

An X-Files story without Mulder and Scully, oh the horror, I know. Of course, Mulder and Scully are there behind the shadows, motivating everything, and I feel that makes it work. I really would have liked to tell a Mulder and Scully story, but it wasn't right for this. Mulder and Scully were off of The X-Files, in hiding and keeping their heads down. But when we see them again in I Want To Believe, Scully is living in the open and Mulder is only half-hiding. They're back in the US. It feels off and I wanted to set up a story to explain their return. For them to return, that means they have to be gone, and the last thing I wanted to do was write a Mulder and Scully romance story that neglected the things that made The X-Files work. I wanted an X-File, a good old classic mythology episode.

So the idea that Doggett and Reyes would mistake a message as being from Mulder and Scully drove the story, with everything suggesting the two agents were going to help them. Instead, all along it was an unused character, Doggett's old friend and super soldier Shannon McMahon, played on the show by Lucy Lawless, attempting to get a meeting with Doggett covertly. A bit of a misunderstanding done to get the pieces in place for the second half of the story, which was never written.

I left the end of the series very frustrated. Many things felt like slaps to the face on old fans, as far as I was concerned, and I thought the ending was awful. Not only ending the series on a clip show, and the "truth" being incoherent ramblings that never really were answers so much as a summary of the series' mysteries, it was a mess that lost sight of the series. So much weight was put on Toothpick Man, Knowle Rohrer, and Gibson Praise, while more familiar characters were paraded like cameos that never fit. Kersh's 11th hour and 45 minute conversion was out of place and out of character, and it was all meant to say "see, he's not such a bad guy!". There's so much I really, really disliked about the ending. And yet, in I Want To Believe, with Whitney's line "All is forgiven", the entire thing was swept away in a second. Just a little misunderstanding. Wow. How could that happen?

This story serves a lot of purposes, mainly as a transition between the end of the series and I Want To Believe. Since then, a new season has come out, a comic book series of Season 10 and 11, and so on. This story does not fit with the comics, but still fits with the new season (which gives me thoughts about how to write the follow-up, actually. Reyes has more story to tell). It's just a beginning, however.

The X-Files was a pre-9/11 series, and was only on in its dying breaths for a few months after the attacks. Writing a post-9/11 X-Files story presented a lot of challenge and opportunity, but that was part of the appeal. 9/11 fueled a lot of conspiracy talk, and that was the stuff The X-Files thrived on. There was a lot of interesting political stuff going on at the time, there was the beginning of two wars, and another interesting turn of events relevant to the series: a new director and restaffing at The FBI. This was perfect for the story, and it gave me a reason for all of the sudden changes that happened between Season Nine and I Want To Believe. A previous FBI administration was corrupted, the War on Terror changed the political landscape enough unexpectedly that some infiltration increased, and others were tossed out, but most importantly, the resources were being redirected toward fighting terrorism. So a new FBI director comes in, sees the Mulder incident with disbelief, and thinks it's a joke that looks bad for the FBI and for the country at a time of crisis. This led to a scene with the new director and AD Skinner discussing these things, and I wrote it almost humorously with the director looking at the series finale.

Introducing a new authority figure to an X-Files story is difficult. You have to walk a line between sinister and trustworthy. This is part of why Kersh was an awful character, there was never a second where he was trustworthy, not an effective boss. He almost felt like a parody. Adding the new director meant partially keeping him in the shadows, he had a big scene to show the changes underway and to effectively end Mulder's death sentence, as well as play catch-up on a few characters, but as a character he needs to be offscreen as much as possible. This might well be the only appearance he should have. Instead, I introduced a new character this season, perhaps a new Krycek. Or perhaps a new Doggett. His nature has yet to be shown, only that he's not around in the new Revival.

Agent Tolson is named for a famous person within the FBI: Clyde Tolson, and I reference this in the story when its implied that his name connects him to the family of that famous figure. There's something sinister any time you bring up Hoover and Tolson to begin with, but Tolson does sort of personify the FBI's role in the series. On one hand, he's an investigator with a lot of respect and confidence, but he's also secretive and may not be what he seems. He serves as a link between the old series and the aftermath and reuniting the characters. He is the FBI itself, basically, calling everyone back.

Reyes is one of the most hated characters, I think. The thing is I never hated her so much as I found the writing for her was awful. She was interesting because she had a bit of Mulder and Scully in her. On one hand, she'll tell you everything about crystal healing or energies, but she'll also scoff at people being possessed by listening to Marilyn Manson albums. She's practically born to pull out her gun and shout "federal agent!", and without being awkward doing so like Dakota Whitney. She's nuts in the way Mulder is nuts, but she's got a lot of guts and is a good investigator when she's not off the deep end. So for this episode, I took her out of the crazy element, but still needed her because there is an X-File here. There needs to be that interest in crazy to drive the plot, and Mulder is off the grid. It's a job for Reyes, and of course it's writer's bias but I think the airport scene is the best thing I've seen Reyes in.

John Doggett was a reluctant member of The X-Files, even though he was totally loyal. He never sought it out, and it wasn't where he wanted to be. I felt that he was an honorable guy, with a bit of pride, and was driven by his son's death. In Release, Doggett resolves his story arc, and in The Truth he's just a background, support character without much use. He was done, and I felt that after witnessing the farce that was the tribunal, he would have lost all faith in the FBI and government, and would have thrown his badge in Kersh's face (not to mention what he would do to the corn flakes!), and left it all. So ultimately I saw a man born for law enforcement who grew disgusted with law enforcement, going back to New York and getting a job away from conspiracies and monsters as a security guard and living alone in a small apartment. And just letting his life go on. Drawing him back was the worst thing I could do to him, and do that's what I did. So he was given a coerced return for the purposes of finding and helping Mulder and Scully. Personally, I thought Doggett was a great character, very different from the other characters and making him a lead here was very important. I thought giving him a place to shine as a character in an old-fashioned kind of episode would show that he was misjudged. In the years since the series ended, I find that view vindicated and the hate for him has really died down. He's the real main character in this story.

I found Kersh's story arc to be unbelievable as much as the character was unlikable. But I ran with it and thought about his actions at the end of the series, and what must have broken in him. To realize that you've been manipulated...by aliens of all things...to kill people and hide the truth. I would think Kersh would be devastated to see his entire life in those terms, and I hated the character to begin with and didn't want to write him in. Killing him off the way I did was in conjunction with Follmer's prosecution, and was a catalyst for bringing the Mulder incident to the director's attention. You don't lose two Deputy Directors in a matter of weeks and not ask questions. To matters worse for Kersh, Skinner reopened the investigation after Mulder's sentencing, meaning all of his involvement and dirty deeds were about to be aired.

The opening teaser is very dark, and was trying to capture something in the show, but also hits on some big fears and there have been events since I wrote this that make it even creepier. I think it hits a lot of nerves. It was the way I could introduce the X-Files in this episode, which was something along the lines of The Thinker's story in Anasazi. In this case, a young UFO enthusiast has been communicating with someone in France who might be Agent Mulder, only to be targeted with an illegal wiretap and surveillance. When local police look into the strange activity, a cop is killed which exposes this, and gets Reyes' attention. Unfortunately, there was too much story to tell to really focus on that aspect, had I written the next part it would have played out in the vein of The Blessing Way/Paper Clip probably. The point of it, however, is to indicate that Mulder is alive, and that he's still working on exposing the truth, and someone is trying to find him. Mulder is The X-File here. Mulder's location is the truth Doggett and Reyes are after, and he is out there.


End file.
